U.S. patent application number 10/695194 was filed with the patent office on 2004-09-02 for diagnostic method for transmissible spongiform encephalopathies.
Invention is credited to Guillaume, Elisabeth, Hochstrasser, Denis Francois, Sanchez, Jean-Charles.
Application Number | 20040171026 10/695194 |
Document ID | / |
Family ID | 32912672 |
Filed Date | 2004-09-02 |
United States Patent
Application |
20040171026 |
Kind Code |
A1 |
Hochstrasser, Denis Francois ;
et al. |
September 2, 2004 |
Diagnostic method for transmissible spongiform encephalopathies
Abstract
Transmissible spongiform encephalopathy (TSE) is diagnosed in a
subject by using mass spectrometry to observe a polypeptide in a
sample of body fluid taken from the subject. The polypeptide is
differentially contained in the body fluid of TSE-infected subjects
and non-infected subjects, and has a molecular weight in the range
of from 1000 to 100000.
Inventors: |
Hochstrasser, Denis Francois;
(Geneva, CH) ; Sanchez, Jean-Charles; (Geneva,
CH) ; Guillaume, Elisabeth; (Annemasse, FR) |
Correspondence
Address: |
BAKER & BOTTS
30 ROCKEFELLER PLAZA
NEW YORK
NY
10112
|
Family ID: |
32912672 |
Appl. No.: |
10/695194 |
Filed: |
October 28, 2003 |
Related U.S. Patent Documents
|
|
|
|
|
|
Application
Number |
Filing Date |
Patent Number |
|
|
10695194 |
Oct 28, 2003 |
|
|
|
PCT/EP02/10063 |
Sep 3, 2002 |
|
|
|
Current U.S.
Class: |
435/6.11 ;
435/6.16 |
Current CPC
Class: |
G01N 2800/2828 20130101;
G01N 33/6896 20130101 |
Class at
Publication: |
435/006 |
International
Class: |
C12Q 001/68 |
Foreign Application Data
Date |
Code |
Application Number |
Sep 5, 2001 |
GB |
01 21459.2 |
Oct 30, 2002 |
GB |
02 25245.0 |
Mar 19, 2003 |
GB |
03 06290.8 |
Claims
I/we claim:
1. A method of diagnosis of a transmissible spongiform
encephalopathy (TSE) or the possibility thereof in a subject
suspected of suffering from the TSE, which comprises subjecting a
sample of body fluid taken from the subject to mass spectrometry,
thereby to determine a test amount of a polypeptide in the sample,
wherein the polypeptide is differentially contained in the body
fluid of TSE-infected subjects and non-TSE-infected subjects, and
has a molecular weight in the range of from 1000 to 100000; and
determining whether the test amount is consistent with a diagnosis
of TSE.
2. A method according to claim 1, in which the polypeptide is
present in the body fluid of TSE-infected subjects and not present
in the body fluid of non-TSE-infected subjects, whereby the
presence of the polypeptide in a body fluid sample is indicative of
TSE.
3. A method according to claim 1, in which the polypeptide is not
present in the body fluid of TSE-infected subjects and present in
the body fluid of non-TSE-infected subjects, whereby the
non-presence of the polypeptide in a body fluid sample is
indicative of TSE.
4. A method according to claim 1, in which the mass spectrometry is
laser desorption/ionization mass spectrometry.
5. A method according to claim 4, in which the sample is adsorbed
on a probe or on a protein chip array having an immobilized metal
affinity capture (IMAC), hydrophobic, strong anionic or weak
cationic exchange surface capable of binding the polypeptide.
6. A method according to claim 4, in which the polypeptide is
determined by surface-enhanced laser desorption/ionization (SELDI)
and time of flight mass spectrometry (TOF-MS).
7. A method according to claim 1, in which the body fluid is
cerebrospinal fluid, plasma, serum, blood, tears, urine or
saliva.
8. A method according to claim 1, in which a plurality of peptides
is determined in the sample.
9. A method according to claim 1, in which the TSE is
Creutzfeldt-Jakob disease (CJD).
10. A method according to claim 9, in which the TSE is sporadic
Creutzfeldt-Jakob Disease (CJD) or variant Creutzfeldt-Jakob
Disease (CJD).
11. A method according to claim 9, in which one or more
polypeptides having a respective molecular weight of about 4780,
about 6700, about 8600 or about 13375 is determined, and the
presence of one or more of such polypeptides is indicative of
CJD.
12. A method according to claim 9 in which one or more polypeptides
having a respective molecular weight of about 3970, about 3990,
about 4294, about 4478, about 10075, about 11730, about 14043 or
about 17839 is determined, and the absence of one or more of such
polypeptides is indicative of CJD.
13. A method according to claim 9, in which a polypeptide having a
molecular weight of about 7770 is determined, and the presence of
such polypeptide is indicative of CJD.
14. A method according to claim 9, in which a polypeptide having a
molecular weight of about 3295, about 4315, about 4436, about 6200,
about 8936, about 9107, about 9145, about 9185, about 9454 or about
13550 Da is determined, and the absence or decreased amount of one
or more of such polypeptides is indicative of CJD.
15. A method according to claim 9, in which a polypeptide having a
molecular weight of about 7574, about 7930, about 7975 or about
8020 Da is determined, and the presence or increased amount of one
or more of such polypeptides is indicative of CID.
16. A method according to claim 1, in which the TSE is Bovine
Spongiform Encephalopathy (BSE).
17. A method according to claim 16, in which the polypeptide has a
molecular weight of about 10220, and the presence of the
polypeptide is indicative of BSE.
18. A method according to claim 16, in which one or more
polypeptides having a respective molecular weight of about 1010,
1100, 1125, 1365, 3645, 4030, 3890, 5820, 7520, 7630, 7980, 9950,
10250, 11600, 11800, 15000, 15200, 15400, 15600, 15900, 30000,
31000 and 31800 Da is determined, and the differential expression
of one or more of such polypeptides is indicative of BSE.
19. A method according to claim 1, in which the TSE is scrapie.
20. A method of diagnosis, prognosis or therapy which comprises use
of a polypeptide which is differentially contained in a body fluid
of TSE-infected subjects and non-infected subjects, the polypeptide
having a molecular weight in the range of from 1000 to 100000 and
being determinable by mass spectrometry.
21. A method of diagnosis, prognosis or therapy which comprises use
of a material which recognizes, binds to or has affinity for a
polypeptide which is differentially contained in a body fluid of
TSE-infected subjects and non-infected subjects, the polypeptide
having a molecular weight in the range of trom 1000 to 100000 and
being determinable by mass spectrometry.
22. A method according to claim 21, in which the material is an
antibody or antibody chip.
23. An assay device for use in the diagnosis of TSE which comprises
a plate having a location containing a material which recognizes,
binds to or has affinity for a polypeptide which is differentially
contained in a body fluid of TSE-infected subjects and non-infected
subjects, the polypeptide having a molecular weight in the range of
from 1000 to 100000 and being determinable by mass
spectrometry.
24. An assay device for use in the diagnosis of TSE, which
comprises a plate having a location containing an antibody that is
specific for Cystatin C.
25. An assay device for use in the diagnosis of variant CJD, which
comprises a plate having a location containing an antibody that is
specific for Cystatin C and useful in the diagnosis of variant
CJD.
26. An assay device for use in the diagnosis of sporadic CJD, which
comprises a plate having a location containing an antibody that is
specific for Cystatin C and useful in the diagnosis of sporadic
CJD.
27. An assay device for use in the diagnosis of BSE, which
comprises a plate having a location containing an antibody that is
specific for a hemoglobin, a hemoglobin chain or a truncated chain
or a fragment thereof having an immunological reaction to
antibodies specific for bovine hemoglobin and useful in the
diagnosis of BSE.
28. An assay device for use in the diagnosis of a TSE comprising a
solid substrate having attached thereto an antibody that is
specific for any of the following: (i) a polypeptide that is
differentially contained in the body fluid of TSE-infected subjects
and non-TSE-infected subjects, and has a molecular weight in the
range of from 1000 to 100000; (ii) a polypeptide that is
differentially contained in the body fluid of TSE-infected subjects
and non-TSE-infected subjects, and is selected from those having a
respective molecular weight of about 1010, 1100, 1125, 1365, 3645,
4030, 3890, 5820, 7520, 7630, 7980, 9950, 10250, 11600, 11800,
15000, 15200, 15400, 15600, 15900, 30000, 31000 and 31800 Da (iii)
cystatin C; (iv) a hemoglobin, a hemoglobin chain or a truncated
chain or a fragment thereof which exhibits an immunological
reaction to an antibody to bovine hemoglobin and is differentially
contained in the body tissue of bovine TSE-infected subjects and
non-bovine non-TSE-infected subjects.
29. A kit for use in diagnosis of TSE, comprising a probe for
receiving a sample of body fluid, and for placement in a mass
spectrometer, thereby to determine a test amount of a polypeptide
in the sample, wherein the polypeptide is differentially contained
in the body fluid of TSE-infected subjects and non-TSE-infected
subjects, and has a molecular weight in the range of from 1000 to
100000.
30. A kit according to claim 29, in which the probe contains an
adsorbent for adsorption of the polypeptide.
31. A kit according to claim 29, further comprising a washing
solution for removal of unbound or weakly bound materials from the
probe.
32. A method of diagnosis of a transmissible spongiform
encephalopathy (TSE) or the possibility thereof in a subject
suspected of suffering from the TSE, which comprises determining a
test amount of a polypeptide in a sample of body fluid taken from
the subject, wherein the polypeptide is differentially contained in
the body fluid of TSE-infected subjects and non-TSE-infected
subjects, and is Cystatin C; and determining whether the test
amount is consistent with a diagnosis of TSE.
33. A method of diagnosis of a transmissible spongiform
encephalopathy (TSE) or the possibility thereof in a subject
suspected of suffering from the TSE, which comprises subjecting a
sample of body fluid taken from the subject to mass spectrometry,
thereby to determine a test amount of a polypeptide in the sample,
wherein the polypeptide is differentially contained in the body
fluid of TSE-infected subjects and non-TSE-infected subjects, and
is Cystatin C; and determining whether the test amount is
consistent with a diagnosis of TSE.
34. The method of claim 33, wherein the body fluid is CSF.
35. A method of diagnosis of a transmissible spongiform
encephalopathy (TSE) or the possibility thereof in a bovine subject
suspected of suffering from the TSE, which comprises determining a
test amount of a polypeptide in a sample of body fluid taken from
the subject, wherein the polypeptide is differentially contained in
the body fluid of TSE-infected bovine subjects and non-TSE-infected
subjects, and is a hemoglobin, a hemoglobin chain or a truncated
chain or a fragment thereof which exhibits an immunological
reaction to an antibody to bovine hemoglobin; and determining
whether the test amount is consistent with a diagnosis of TSE.
36. A method of diagnosis of a transmissible spongiform
encephalopathy (TSE) or the possibility thereof in a bovine subject
suspected of suffering from the TSE, which comprises subjecting a
sample of body fluid taken from the subject to mass spectrometry,
thereby to determine a test amount of a polypeptide in the sample,
wherein the polypeptide is differentially contained in the body
fluid of TSE-infected bovine subjects and non-TSE-infected
subjects, and is a hemoglobin, a hemoglobin chain or a truncated
chain or a fragment thereof which exhibits an immunological
reaction to an antibody to bovine hemoglobin; and determining
whether the test amount is consistent with a diagnosis of TSE.
37. A method of providing an indication of a transmissible
spongiform encephalopathy (TSE) or the possibility or progress
thereof in a subject liable to suffer from the TSE, which comprises
use as a marker of a level of at least one polypeptide that has a
molecular weight in the range of from 1000 to 100000, is measurable
or detectable in the body tissue by mass spectrometry and is
differentially contained in the body fluid of TSE-infected subjects
and non-TSE-infected subjects.
38. The method of claim 37, wherein said at least one polypeptide
is selected from those having a respective molecular weight of
about 1010, 1100, 1125, 1365, 3645, 4030, 3890, 5820, 7520, 7630,
7980, 9950, 10250, 11600, 11800, 15000, 15200, 15400, 15600, 15900,
30000, 31000 and 31800 Da.
39. The method of claim 37, in which the body fluid is
cerebrospinal fluid, plasma, serum, blood, tears, urine or
saliva.
40. A method of providing an indication of a transmissible
spongiform encephalopathy (TSE) or the possibility or progress
thereof in a subject liable to suffer from the TSE, which comprises
use as a marker of a level of cystatin C measurable or detectable
in a sample of body tissue by mass spectroscopy and differentially
contained in the body tissue offSE-infected subjects and
non-TSE-infected subjects.
41. The method of claim 40, wherein the body tissue is from a human
subject.
42. The method of claim 40, wherein the body tissue is
cerebrospinal fluid.
43. A method of providing an indication of a transmissible
spongiform encephalopathy (TSE) or the possibility or progress
thereof in a bovine subject liable to suffer from the TSE, which
comprises use as a marker of a level of a hemoglobin, a hemoglobin
chain or a truncated chain or a fragment thereof which exhibits an
immunological reaction to an antibody to bovine hemoglobin, said
level being measurable or detectable in a sample of body tissue by
mass spectroscopy, and said hemoglobin, hemoglobin chain or
truncated chain or fragment thereof being differentially contained
in the body tissue of bovine TSE-infected subjects and non-bovine
non-TSE-infected subjects.
44. The method of claim 43, wherein said hemoglobin, hemoglobin
chain or truncated chain or fragment thereof has a molecular weight
determinable by mass spectroscopy of about 15000 Da, 7500 Da or
3000 Da.
45. The method of claim 43, wherein the sample of body tissue is
plasma.
46. The method of claim 43, wherein the sample of body tissue is
from a living animal.
47. A bovine animal, or herd of said animals, that has or have been
subjected to a test as defined in claim 43 and found to be free of
a transmissible spongiform encephalopathy (TSE).
Description
BACKGROUND OF THE INVENTION
[0001] This application is a continuation-in-part application of
International Patent Application No. PCT/EP02/10063, filed Sep. 3,
2002 and published on Mar. 20, 2003 as WO03/023406, which claims
priority from UK Patent Application No. 01 21459.2, filed Sep. 5,
2001.
FIELD OF THE INVENTION
[0002] This invention relates to a method for obtaining information
that may have utility in providing an indication of the presence of
a transmissible spongiform encephalopathy (TSE) or the possibility
or progress thereof.
DESCRIPTION OF THE RELATED ART
[0003] Transmissible spongiform encephalopathies (TSEs) are
neurodegenerative diseases of the central nervous system. They can
be transmitted, inherited or occur sporadically and are observed in
animals, e.g., as bovine spongiform encephalopathy (BSE) in cattle
or scrapie in sheep, as well as in humans as Creutzfeldt-Jakob
disease (CJD), Gerstman Strussler Scheinker syndrome, Fatal
Familial Insomnia or Kuru. They have a long incubation period,
leading to ataxia, dementia, psychiatric disturbances and death.
Neuropathological changes include vacuolar degeneration of brain
tissue, astrogliosis and amyloid plaque formation. The diseases are
difficult to diagnose pre-mortem.
[0004] The cerebrospinal fluid (CSF) of CJD patients displays two
additional polypeptides (known as 14-3-3 polypeptides) by
two-dimensional polyacrylamide gel electrophoresis [Harrington, M.
G. New England Journal of Medicine 315, 279 (1986), Hsich, G.,
Kenney, K., Gibbs, C. J., Lee, K. H. & Harrington, M. B., New
England Journal of Medicine 335, 924 (1996).] The function of these
14-3-3 polypeptides remains unclear in TSE. They can be used in a
pre-mortem test for CJD diagnostic evaluation, but have low
specificity.
[0005] Monoclonal antibodies to the abnormal form of prion protein
(which is associated with CJD) are available and can be used in an
enzyme-linked immunoassay, as described in PCT Specifications WO
98/23962 and 98/32710 and Schmerr, M. J., the Beckman Coulter Pace
Setter Newsletter 3(2), 1-4 (June 1999), but these procedures have
not yet been fully developed.
[0006] WO 01/67108 relates to a diagnostic assay for TSEs in which
the concentration of heart or brain fatty acid binding protein
(H-FABP or B-FABP) is determined in a sample of body fluid.
[0007] U.S. Pat. No. 6,225,047 describes the use of retentate
chromatography to generate difference maps, and in particular a
method of identifying analytes that are differentially present
between two samples. One specific method described therein is laser
desorption mass spectrometry.
[0008] WO 01/25791 describes a method for aiding a prostate cancer
diagnosis, which comprises determining a test amount of a
polypeptide marker, which is differentially present in samples of a
prostate cancer patient and a subject who does not have prostate
cancer. The marker may be determined using mass spectrometry, and
preferably laser desorption mass spectrometry.
[0009] Development of new non-invasive TSE markers for body fluids
or other body tissues (in particular, CJD and BSE markers in blood)
and new methods of determining the markers would help clinicians to
establish early diagnosis. This problem has now been solved by the
present invention.
SUMMARY OF THE INVENTION
[0010] The present invention provides a method of diagnosis of a
transmissible spongiform encephalopathy (TSE) or the possibility
thereof in a subject suspected of suffering from the TSE, which
comprises subjecting a sample of body fluid taken from the subject
to mass spectrometry, thereby to determine a test amount of a
polypeptide in the sample, wherein the polypeptide is
differentially contained in the body fluid of TSE-infected subjects
and non-TSE-infected subjects, and has a molecular weight in the
range of from 1000 to 100000; and determining whether the test
amount is consistent with a diagnosis of TSE.
[0011] The invention also provides use of a polypeptide which is
differentially contained in a body fluid of TSE-infected subjects
and non-infected subjects, the polypeptide having a molecular
weight in the range of from 1000 to 100000 and being determinable
by mass spectrometry, for diagnostic, prognostic and therapeutic
applications.
[0012] In embodiments of the invention, the molecular weight may,
for example, be from 1000 to less than 3500, from 3500 to 30000, or
from above 30000 to 100000.
[0013] The invention further relates to the use of a marker of
molecular weight about 13350, reported in our application
GB-A-2379737, in a method of diagnosis of a transmissible
spongiform encephalopathy (TSE) or the possibility thereof in a
subject suspected of suffering from TSE. That marker is believed to
be cystatin C (Swiss-Prot Accession NO: P01034, active protein of
120 AA, theoretical pI of 8.75) also called Neuroendocrine basic
polypeptide, Gamma Trace or Post gamma globulin. This secreted
active inhibitor of cysteine proteinases belongs to a super-family
of proteins that includes 3 groups on the basis of similar sequence
and structural properties. This protein is highly expressed in the
epididymis, vas deferens, brain, thymus, and ovary and at a lower
level in the submandibular gland. Cystatin C has been confirmed by
immunoblotting to be differentially expressed in the CSF of CJD
affected patients. It is derived from a precursor having the
sequence (SEQ ID No: 1):
1 magplrapll llailavala vspaagsspg kpprlvggpm dasveeegvr raldfavgey
60 nkasndmyhs ralqvvrark qivagvnyfl dvelgrttct ktqpnldncp
fhdqphlkrk 120 afcsfqiyav pwqgtmtlsk stcqda 146
[0014] and has the sequence (SEQ ID No: 2) set out below:
2 sspgkpprlv ggpmdasvee egvrraldfa vgeynkasnd myhsralqvv rarkqivagv
60 nyfldvelgr ttctktqpnl dncpfhdqph lkrkafcsfq iyavpwqgtm
tlskstcqda 120
[0015] A mutant form of cystatin C (Leu to Glu substitution in 68)
has been described as being implicated in a hereditary form of
cerebral hemorrhage characterized by a thickening of the cerebral
artery walls, with deposition of material with the characteristics
of amyloid. There are also some genotypes (BB: Ala to Thr
substitution) associated with increased risk of late onset of
Alzheimer disease.
[0016] The invention therefore provides a method of diagnosis of a
transmissible spongiform encephalopathy (TSE) or the possibility
thereof in a subject suspected of suffering from the TSE, which
comprises subjecting a sample of body fluid taken from the subject
to mass spectrometry, thereby to determine a test amount of a
polypeptide in the sample, wherein the polypeptide is
differentially contained in the body fluid of TSE-infected subjects
and non-TSE-infected subjects, and is cystatin C; and determining
whether the test amount is consistent with a diagnosis of TSE. The
body fluid is preferably cerebrospinal fluid but may be whole
blood, plasma, serum, urine or a tissue in which prion proteins
tend to accumulate, e.g., the tonsil and other tissues of the
lympho-reticular system such as the lymph nodes.
[0017] The invention further provides the use of a level of
cystatin C measurable or detectable in a sample of body tissue by
mass spectroscopy and differentially contained in the body tissue
of TSE-infected subjects and non-TSE-infected subjects as a marker
for providing an indication of a transmissible spongiform
encephalopathy (TSE) or the possibility or progress thereof in a
subject liable to suffer from the TSE.
[0018] In further experiments the inventors have identified and
validated various hemoglobin isoforms as being the main protein
able to discriminate between BSE+ and BSE-affected cattle using
laser desorption/ionization mass spectrometry. In SELDI mass
spectroscopy peaks or clusters at about 30,000, 15000 Da, 7500 Da
may be indicative of hemoglobin, and these may correspond to a
substantially intact hemoglobin molecule with a multiple electrical
charge, or it may be a hemoglobin chain or a truncated version or
fragment thereof having an immunological reaction to antibodies
specific for bovine hemoglobin. The presence or absence of
hemoglobin peaks or clusters in a SELDI spectrum therefore provides
a means for ante-mortem diagnosis for BSE in cattle e.g., by tests
carried out on plasma or other body fluids.
[0019] In a further aspect, therefore, the invention provides a
method of diagnosis of a transmissible spongiform encephalopathy
(TSE) or the possibility thereof in a bovine subject suspected of
suffering from the TSE, which comprises subjecting a sample of body
fluid taken from the subject to mass spectrometry, thereby to
determine a test amount of a polypeptide in the sample, wherein the
polypeptide is differentially contained in the body fluid of
TSE-infected bovine subjects and non-TSE-infected subjects, and is
a hemoglobin, a hemoglobin chain or a truncated chain or a fragment
thereof thereof having an immunological reaction to antibodies
specific for bovine hemoglobin; and determining whether the test
amount is consistent with a diagnosis of TSE.
[0020] As used herein the expression "bovine" shall include cattle
generally, sheep (scrapie) and also deer and elk (chronic wasting
disease).
[0021] The invention further provides the use of a level of a
hemoglobin, a hemoglobin chain or a truncated chain or a fragment
thereof having an immunological reaction to antibodies specific for
bovine hemoglobin, said level being measurable or detectable in a
sample of body tissue by mass spectroscopy and said a hemoglobin, a
hemoglobin chain or a truncated chain or a fragment thereof which
exhibits an immunological reaction to an antibody to bovine
hemoglobin being differentially contained in the body tissue of
bovine TSE-infected subjects and non-bovine non-TSE-infected
subjects as a marker for providing an indication of a transmissible
spongiform encephalopathy (TSE) or the possibility or progress
thereof in a bovine subject liable to suffer from the TSE.
[0022] The above test will be of value when applied to an animal or
herd of animals either on a single occasion or at intervals, and
animals that have been found not to be suffering from an actual or
latent transmissible spongiform encephalopathy will self-evidently
be of enhanced value. Such animals and the method of testing them
are also within the scope of the invention.
[0023] The invention further provides assay devices or kits for use
in the diagnosis of a TSE comprising a solid substrate having
attached thereto an antibody that is specific for any of the
following:
[0024] (i) a polypeptide that is differentially contained in the
body fluid of TSE-infected subjects and non-TSE-infected subjects,
and has a molecular weight in the range of from 1000 to 100000;
[0025] (ii) a polypeptide that is differentially contained in the
body fluid of TSE-infected subjects and non-TSE-infected subjects,
and is selected from those having a respective molecular weight of
about 1010, 1100, 1125, 1365, 3645, 4030, 3890, 5820, 7520, 7630,
7980, 9950, 10250, 11600, 11800, 15000, 15200, 15400, 15600, 15900,
30000, 31000 and 31800 Da.;
[0026] (iii) cystatin C;
[0027] (iv) a hemoglobin, a hemoglobin chain or a truncated chain
or a fragment thereof which exhibits an immunological reaction to
an antibody to bovine hemoglobin and is differentially contained in
the body tissue of bovine TSE-infected subjects and non-bovine
non-TSE-infected subjects. The above devices or kits may further
comprise necessary preparative reagents, washing reagents,
detection reagents and signal producing reagents.
[0028] The invention also further provides an assay device for use
in the diagnosis of TSE which comprises any of
[0029] a plate having a location containing a material which
recognizes, binds to or has affinity for a polypeptide which is
differentially contained in a body fluid of TSE-infected subjects
and non-infected subjects, the polypeptide having a molecular
weight in the range of from 1000 to 100000 and being determinable
by mass spectrometry;
[0030] a plate having a location containing an antibody that is
specific for Cystatin C;
[0031] a plate having a location containing an antibody that is
specific for Cystatin C and useful in the diagnosis of variant
CJD;
[0032] a plate having a location containing an antibody that is
specific for Cystatin C and useful in the diagnosis of sporadic
CJD.
[0033] The above devices may also be provided in association with
necessary preparative reagents, washing reagents, detection
reagents and signal producing reagents.
[0034] The invention further provides a kit for use in diagnosis of
TSE, comprising a probe or a protein chip array for receiving a
sample of body fluid, and for placement in a mass spectrometer,
thereby to determine a test amount of a polypeptide in the sample,
wherein the polypeptide is differentially contained in the body
fluid of TSE-infected subjects and non-TSE-infected subjects, and
has a molecular weight in the range of from 1000 to 100000.
BRIEF DESCRIPTION OF THE DRAWINGS
[0035] FIG. 1 is a spectral view of CSF from normal and
CJD-infected samples using laser desorption/ionization mass
spectrometry;
[0036] FIG. 2 is a corresponding view highlighting a protein peak
at about 4780 Da in CJD-infected CSF samples;
[0037] FIG. 3 is a corresponding view highlighting protein peaks at
about 6700 and 8600 Da in CJD-infected CSF samples;
[0038] FIG. 4 is a corresponding view highlighting a protein peak
at about 13375 Da in CJD-infected CSF samples;
[0039] FIG. 5 is a spectral view of plasma from normal and
BSE-infected samples using laser desorption/ionization mass
spectrometry;
[0040] FIG. 6 is a view corresponding to FIG. 5 and highlighting a
protein peak at about 10220 Da in BSE-infected plasma samples;
[0041] FIG. 7 is a spectral view of plasma from CJD-infected
patients (CJD+) and non-infected patients (CJD-) using laser
desorption/ionization mass spectrometry;
[0042] FIGS. 8A and 8B are views corresponding to FIG. 7 and
highlighting polypeptide peaks that are differentially expressed in
the CJD+ and CJD- plasma samples;
[0043] FIGS. 9A to 9E are spectral views of plasma from
CJD-infected patients (plasma CJD) and non-infected patients
(plasma CTS) highlighting further polypeptide peaks that are
differentially expressed in the infected and non-infected
samples.
[0044] FIGS. 10A to 10F OF are spectral views of plasma from normal
and BSE-infected samples using laser desorption/ionization mass
spectrometry, highlighting protein peaks at about 1010, 1100, 1125,
1365, 3645, 4030, 3890, 5820, 7520, 7630, 7980, 9950, 10250, 11600,
11800, 15000, 15200, 15400, 15600, 15900, 30000, 31000 and 31800 Da
in plasma samples;
[0045] FIG. 11 shows human cystatin C immunodetection in CSF
samples;
[0046] FIG. 12 shows bovine hemoglobin detection in plasma
samples;
[0047] FIG. 13 shows a BSE plasma sample on a two-dimensional gel
and on a two-dimensional PVDF membrane;
[0048] FIG. 14 shows spectra of human and bovine hemoglobin using
laser desorption/ionization mass spectrometry; and
[0049] FIGS. 15A to 15C show spectra from plasma from normal bovine
and BSE-infected samples using laser desorption/ionization mass
spectrometry.
DESCRIPTION OF PREFERRED EMBODIMENTS
[0050] The invention provides a method of diagnosis of a
transmissible spongiform encephalopathy (TSE) or the possibility
thereof in a subject suspected of suffering from the TSE. A sample
of body fluid taken from the subject is subjected to mass
spectrometry, to determine the presence or absence in the sample of
a polypeptide marker, which is differentially contained in the body
fluid of TSE-infected subjects and non-infected subjects. The
polypeptide marker has a molecular weight in the range of from 1000
to 100000, preferably from 1000 to 35000, and the presence,
absence, under-expression or over-expression of the marker is
indicative of TSE.
[0051] The method is applicable to all types of TSE, and to any
human or animal suffering or suspected of suffering therefrom. The
method is especially applicable to the diagnosis of CJD, especially
new variant CJD, in human patients, and to BSE in ruminant animals
such as cattle, and to BSE-like diseases in other animals, such as
scrapie in sheep.
[0052] The term polypeptide includes proteins and protein
fragments, as well as peptides modified by the addition of
non-peptide residues, e.g., carbohydrates, phosphates, sulfates or
any other post-translational modification.
[0053] The sample may be adsorbed on a probe under conditions which
allow binding between the polypeptide and adsorbent material on the
probe or the protein chip array. The adsorbent material preferably
comprises a metal chelating group complexed with a metal ion, and a
preferred metal is copper. Prior to detecting the polypeptide,
unbound or weakly bound materials on the probe or protein chip
array may be removed with a washing solution, thereby enriching the
polypeptide in the sample. The sample is preferably adsorbed on a
probe or protein chip array having an immobilized metal affinity
capture (IMAC) surface capable of binding the polypeptide. The
sample may be also adsorbed on a probe having hydrophobic, strong
anionic or weak cationic exchange surfaces under conditions which
allow binding of the polypeptides. The probe may consist of a strip
having several adsorbent wells, and be inserted into the
spectrometer, then movable therein so that each well is in turn
struck by the ionizing means (e.g., laser) to give a spectrometer
reading. The polypeptide is preferably determined by
surface-enhanced laser desorption/ionization (SELDI) and time of
flight mass spectrometry (TOF-MS).
[0054] In principle, any body fluid or tissue can be used to
provide a sample for diagnosis, but preferably the body fluid is
cerebrospinal fluid (CSF), plasma, serum, blood, urine, saliva or
tears.
[0055] In one embodiment of the invention, the TSE is
Creutzfeldt-Jakob disease (CJD). In this case, the polypeptide
preferably has a molecular weight of about 4780, about 6700, about
8600 or about 13375, and the presence of one or more of such
polypeptides is indicative of CJD. Alternatively, one or more
polypeptides having a respective molecular weight of about 3970,
about 3990, about 4294, about 4478, about 10075, about 11730, about
14043 or about 17839 is determined, and the absence of one or more
of such polypeptides is indicative of CJD. As a further
alternative, a polypeptide having a molecular weight of about 7770
is determined, and the presence of such polypeptide is indicative
of CJD. According to one more example, CJD is indicated by a
decrease in a peak at one or more of the following: about 3295,
about 4315, about 4436, about 6200, about 8936, about 9107, about
9145, about 9185, about 9454 and about 13550 Da. According to yet a
further example, CJD is indicated by an increase in a peak at one
or more of the following: about 7574, about 7930, about 7975 and
about 8020. It will be appreciated that the invention embraces
making a measurement at any one or more of the foregoing molecular
weight values, in any combination thereof, for the purpose of
making a diagnosis of CJD.
[0056] In another embodiment of the invention, the TSE is bovine
spongiform encephalopathy (BSE). In this case, the polypeptide
preferably has a molecular weight of about 10220, and the presence
of the polypeptide is indicative of BSE.
[0057] In a further embodiment of the invention, the TSE is bovine
spongiform encephalopathy (BSE). In this case, the polypeptide
preferably has a molecular weight of about 1010, 1100, 1125, 1365,
3645, 4030, 3890, 5820, 7520, 7630, 7980, 9950, 10250, 11600,
11800, 15000, 15200, 15400, 15600, 15900, 30000, 31000 and 31800 Da
and the presence, absence, over-expression or under-expression of
the polypeptide is indicative of BSE.
[0058] In a still further embodiment of the invention, the TSE is
scrapie.
[0059] Measurement of the molecular weight of the polypeptide or
polypeptides is effected in the mass spectrometer. All molecular
weights herein are measured in Da. The molecular weights quoted
above can be measured with an accuracy of better than 1%, generally
0.5 to 1%, and preferably to within about 0.1%. The term "about" in
connection with molecular weights in this specification therefore
means within a variation of about 1%, preferably 0.5%, and more
preferably within about 0.1%, above or below the quoted value.
[0060] The invention also relates to the use of a polypeptide which
is differentially contained in a body fluid of TSE-infected
subjects and non-infected subjects, the polypeptide having a
molecular weight in the range of from 1000 to 100000 and being
determinable by mass spectrometry, for diagnostic, prognostic and
therapeutic applications. This may involve the preparation and/or
use of a material, which recognizes, binds to or has some affinity
to the above-mentioned polypeptide. Examples of such materials are
antibodies and antibody chips. The term "antibody" as used herein
includes polyclonal antiserum, monoclonal antibodies, fragments of
antibodies such as Fab, and genetically engineered antibodies. The
antibodies may be chimeric or of a single species. The above
reference to "prognostic" applications includes making a
determination of the likely course of a TSE by, for example,
measuring the amount of the above-mentioned polypeptide in a sample
of body fluid. The above reference to "therapeutic" applications
includes, for example, preparing materials which recognize, bind to
or have affinity to the above-mentioned polypeptides, and using
such materials in therapy. The materials may in this case be
modified, for example by combining an antibody with a drug, thereby
to target the drug to a specific region of the animal to be
treated.
[0061] The methodology of this invention can be applied to the
diagnosis of any TSE. Body fluid samples are prepared from infected
and non-infected subjects. The samples are applied to a probe or
array having a surface treated with a variety of adsorbent media,
for differential retention of peptides in the sample, optionally
using washing liquids to remove unbound or weakly bound materials.
If appropriate, energy-absorbing material can also be applied. The
probe or array is then inserted into a mass spectrometer, and
readings are taken for the various sample/adsorbent combinations
using a variety of spectrometer settings. Comparison of the
infected and non-infected samples under a given set of conditions
reveals one or more polypeptides, which are differentially
expressed in the infected and non-infected samples. The presence or
absence of these polypeptides can then be used in the testing of a
fluid sample from a subject under the same conditions (adsorbent,
spectrometer settings, etc.) to determine whether or not the
subject is infected.
[0062] References herein to "presence or absence" of a polypeptide
should be understood to mean simply that there is a significant
difference in the amount of a polypeptide which is detected in the
infected and non-infected sample. Thus, the "absence" of a
polypeptide in a test sample may include the possibility that the
polypeptide is actually present, but in a significantly lower
amount than in a comparative test sample. According to the
invention, a diagnosis can be made on the basis of the presence or
absence of a polypeptide, and this includes the presence of a
polypeptide in a significantly lower or significantly higher amount
with reference to a comparative test sample.
[0063] The following Examples illustrate the invention.
EXAMPLE 1
[0064] Polypeptides in Body Fluids (Cerebrospinal Fluid, Plasma and
Others) of Creutzfeld-Jacob-Affected Patients
[0065] The objective of the present study was to detect specific
polypeptides in body fluids (cerebrospinal fluid, plasma and
others) of Creutzfeld-Jacob-affected patients. Samples were
analyzed by the Surface Enhanced Laser Desorption Ionization
(SELDI) Mass Spectroscopy (MS) technology. This technology
encompasses micro-scale affinity capture of proteins by using
different types of retentate chromatography and then analysis by
time of flight mass spectrometry. Different maps are thus generated
each corresponding to a typical protein profiling of given samples
that were analyzed with a Ciphergen Biosystem PBS II mass
spectrometer (Freemont, Calif., USA). Differential expressed peaks
were identified when comparing spectra generated in a group of
cerebrospinal fluid (CSF) samples from CJD-affected patients with a
group of dementia-affected patients.
[0066] The SELDI analysis was performed using 21 .mu.l of crude
human CSF samples in order to detect specific polypeptides with
metal affinity. An immobilized copper affinity array
(IMAC-Cu.sup.++) was employed in this approach to capture proteins
with affinity for copper to select for a specific subset of
proteins from the samples. Captured proteins were directly detected
using the PBSII Protein Chip Array reader (Ciphergen Biosystems,
Freemont, Calif., USA).
[0067] The following protocol was used for the processing and
analysis of ProteinChip arrays using Chromatographic TED-Cu(II)
adsorbent array. TED is a (tris(carboxymethyl) ethylenediamine-Cu)
adsorbent coated on a silicon oxide-coated stainless steel
substrate.
[0068] The surface was first loaded with 1011 of 100 mM copper
sulfate to each spot and incubated for 15 minutes in a wet
chamber.
[0069] The chip was thereafter washed by two quick rinses with
deionized water for about 10 seconds to remove the excess unbound
copper.
[0070] Before loading the samples, the I-MAC 3 array was
equilibrated once with 5 .mu.l of PBS NaCl 0.5 M for 5 minutes.
[0071] After removing the equilibration buffer, 3 .mu.l of the same
buffer were added before applying 2 .mu.l of CSF. The chip was
incubated for 20 minutes in a wet chamber.
[0072] The samples were thereafter removed and the surface was
washed three times with the equilibration buffer (5 minutes
each).
[0073] Two quick final rinses with water were performed.
[0074] The surface was allowed to air dry, followed by the addition
of 0.5 .mu.l of saturated sinapinic acid (SPA, Ciphergen Biosystem)
prepared in 50% acetonitrile, 0.5% trifluoroacetic acid.
[0075] The chip was air dried again before analysis of the retained
protein on each spot with laser desorption/ionization
time-of-flight mass spectrometry.
[0076] The protein chip array was inserted into the instrument and
analyzed once the appropriate detector sensitivity and laser energy
have been established to automate the data collection.
[0077] The obtained spectra were analyzed with the Biomark Wizard
software (Ciphergen Biosystems, Freemont, Calif., USA) running on a
Dell Dimension 4100 PC. It generates consistent peak sets across
multiple spectra.
[0078] FIGS. 1 to 4 show the results of a comparative study which
has been undertaken between CSF from CJD-diagnosed patients and
normal CSF, using the IMAC 3 protein chip array prepared as
described above. In this study, we found that four peaks were
significantly differentially increased in CSF from CJD-affected
patients. Their molecular weights are respectively about 4780,
6700, 8600 and 13375 (mass accuracy is around 0.1%). FIG. 1 shows
two spectral views, respectively, of the normal and CJD sample,
from 0 to 100,000 Da. FIG. 2 shows the protein peak of 4780 Da,
FIG. 3 shows the protein peaks of 6700 and 8600 Da, and FIG. 4
shows the protein peak of 13375 Da. These data demonstrate that the
peaks of about 4780, 6700, 8600 and 13375 Da can be used to
diagnose CJD in CSF samples.
EXAMPLE 2
[0079] Polypeptides in Plasma Samples from BSE-Infected Cattle and
Non-Infected Cattle
[0080] Example 1 was repeated using plasma samples from
BSE-infected cattle (BSE+) and non-infected cattle (BSE-). The
results are shown in FIGS. 5 and 6. FIG. 5 shows a spectral view of
each kind of sample from 0 to 50,000 Da. We observed that a protein
around 10220 Da was significantly increased in BSE+plasma samples,
as illustrated in FIG. 6. This demonstrates that the peak of about
10220 Da can be used to diagnose BSE in plasma samples.
EXAMPLE 3
[0081] Polypeptides in Plasma Samples from CJD-Infected Patients
and Non-Infected Patients
[0082] Example 2 was repeated using plasma samples from
CJD-infected patients (CJD+) and non-infected patients (CJD-, also
referred to as CTS=Swiss Transfusion Centre). The results are shown
in FIGS. 7 and 8. FIG. 7 shows a spectral view of each kind of
sample from 0 to 50,000 Da. We observed that polypeptides of about
3970, about 3990, about 4294, about 4478, about 10075, about 11730,
about 14043 or about 17839 were significantly decreased in
CJD+plasma samples, as illustrated in FIGS. 8A and B. We also
observed that a peak of about 7770 Da was increased in CJD+plasma
samples, as illustrated in FIG. 8B. This demonstrates that the peak
of about 3970, about 3990, about 4294, about 4478, about 10075,
about 11730, about 14043, about 17839 or about 7770 Da can be used
to diagnose CJD in plasma samples.
EXAMPLE 4
[0083] Polypeptides in Plasma Samples from CJD-Infected Patients
and Non-Infected Patients
[0084] Example 3 was repeated, but using a more recent version of
the software to analyse the data. The results are shown in FIGS. 9A
to 9E, and indicate some new variations in protein levels, in
addition to those identified in preceding Examples.
[0085] In FIG. 9A, the arrow indicates a peak at about 3295 Da,
which is decreased in the CJD samples.
[0086] In FIG. 9B, the arrows in order from the left-hand side show
the following:
[0087] 1--a peak at about 3976 Da, which is decreased in the CJD
samples (corresponding to the 3970 Da peak in Example 3)
[0088] 2--a peak at about 3992 Da, which is decreased in the CJD
samples (corresponding to the 3990 Da peak in Example 3)
[0089] 3--a peak at about 4300 Da, which is decreased in the CJD
samples (corresponding to the 4294 Da peak in Example 3)
[0090] 4--a peak at about 4315 Da, which is decreased in the CJD
samples
[0091] 5--a peak at about 4436 Da, which is decreased in the CJD
samples
[0092] 6--a peak at about 4484 Da, which is decreased in the CJD
samples (corresponding to the 4478 Da peak in Example 3)
[0093] In FIG. 9C, the arrow indicates a peak at about 6200 Da,
which is decreased in the CJD samples.
[0094] In FIG. 9D, the arrows in order from the left-hand side show
the following:
[0095] 10--a peak at about 7574 Da, which is increased in the CJD
samples
[0096] 11--a peak at about 7773 Da, which is increased in the CJD
samples (corresponding to the 7770 Da peak in Example 3)
[0097] 12--a peak at about 7930 Da, which is increased in the CJD
samples
[0098] 13--a peak at about 7975 Da, which is increased in the CJD
samples
[0099] 14--a peak at about 8020 Da, which is increased in the CJD
samples
[0100] 15--a peak at about 8936 Da, which is decreased in the CJD
samples
[0101] 16--a peak at about 9107 Da, which is decreased in the CJD
samples
[0102] 17--a peak at about 9145 Da, which is decreased in the CJD
samples
[0103] 18--a peak at about 9185 Da, which is decreased in the CJD
samples
[0104] 19--a peak at about 9454 Da, which is decreased in the CJD
samples
[0105] In FIG. 9E, the arrows in order from the left-hand side show
the following:
[0106] 20--a peak at about 10068 Da, which is decreased in the CJD
samples (corresponding to the 10075 Da peak in Example 3)
[0107] 21--a peak at about 13550 Da, which is decreased in the CJD
samples
[0108] 22--a peak at about 17809 Da, which is decreased in the CJD
samples (corresponding to the 17839 Da peak in Example 3)
[0109] This Example demonstrates that any one of the above peaks,
or more than one of them in any combination, can be used to
diagnose CJD.
EXAMPLE 5
[0110] Polypeptides in Body Fluids (Cerebrospinal Fluid, Plasma and
Others) of BSE-Affected Cattle
[0111] The objective of the present study was to detect specific
polypeptides in body fluids (cerebrospinal fluid, plasma and
others) of BSE-affected cattle. Samples were analyzed by the
Surface Enhanced Laser Desorption Ionization (SELDI) Mass
Spectroscopy (MS) technology. This technology encompasses
micro-scale affinity capture of proteins by using different types
of retentate chromatography and then analysis by time of flight
mass spectrometry. Different maps are thus generated each
corresponding to a typical protein profiling of given samples that
were analyzed with a Ciphergen Biosystem PBS II mass spectrometer
(Freemont, Calif., USA). Differential expressed peaks were
identified when comparing spectra generated in a group of plasma
samples from BSE-affected cattle with a group of healthy cattle
using protein chip arrays.
[0112] The SELDI analysis was performed using 2 .mu.l of crude
bovine plasma samples in order to detect specific polypeptides with
metal affinity. An immobilized copper affinity array
(IMAC-Cu.sup.++) was employed in this approach to capture proteins
with affinity for copper to select for a specific subset of
proteins from the samples. It will be appreciated that other
protein chip arrays and immobilized metal chip arrays may be
substituted for the IMAC-Cu.sup.++ affinity array. Captured
proteins were directly detected using the PBSII Protein Chip Array
reader (Ciphergen Biosystems, Freemont, Calif., USA).
[0113] The following protocol was used for the processing and
analysis of ProteinChip arrays using Chromatographic TED-Cu(II)
adsorbent array. TED is a (tris(carboxymethyl) ethylenediamine-Cu)
adsorbent coated on a silicon oxide-coated stainless steel
substrate.
[0114] The surface was first loaded with 10 .mu.l of 100 mM copper
sulfate to each spot and incubated for 15 minutes in a wet
chamber.
[0115] The chip was thereafter washed by two quick rinses with
deionized water for about 10 seconds to remove the excess unbound
copper.
[0116] Before loading the samples, the I-MAC 3 array was
equilibrated once with 5 .mu.l of PBS NaCl 0.5 M for 5 minutes.
[0117] After removing the equilibration buffer, 3 .mu.l of the same
buffer were added before applying 211 of plasma. The chip was
incubated for 20 minutes in a wet chamber.
[0118] The samples were thereafter removed and the surface was
washed three times with the equilibration buffer (5 minutes
each).
[0119] Two quick final rinses with water were performed.
[0120] The surface was allowed to air dry, followed by the addition
of 0.5 .mu.l of saturated sinapinic acid (SPA, Ciphergen Biosystem)
prepared in 50% acetonitrile, 0.5% trifluoroacetic acid.
[0121] The chip was air dried again before analysis of the retained
protein on each spot with laser desorption/ionization
time-of-flight mass spectrometry.
[0122] The protein chip array was inserted into the instrument and
analyzed once the appropriate detector sensitivity and laser energy
have been established to automate the data collection.
[0123] The obtained spectra were analyzed with the Biomark Wizard
software (Ciphergen Biosystems, Freemont, Calif., USA) running on a
Dell Dimension 4100 PC. It generates consistent peak sets across
multiple spectra.
[0124] FIGS. 10A-10F show the results of a comparative study, which
has been undertaken between plasma from BSE-diagnosed cattle and
normal plasma, using the IMAC3 protein chip array prepared as
described above. In this study, we found that 23 peaks were
significantly differentially expressed in plasma from BSE-affected
cattle. Their molecular weights are, respectively about 1010, 1100,
1125, 1365, 3645, 4030, 3890, 5820, 7520, 7630, 7980, 9950, 10250,
11600, 11800, 15000, 15200, 15400, 15600, 15900, 30000, 31000 and
31800 Da (mass accuracy is around 0.1%). FIG. 10 shows two spectral
views, respectively, of the normal and BSE samples, from 0 to
100,000 Da. More specifically, as indicated by the vertical arrows,
FIG. 10A shows the peaks at about 1010, 1100, 1125 and 1365. FIG.
10B shows the peaks at about 3645 and 4030. FIG. 10C shows the
peaks at about 3890, 5820, 7520, 7630 and 7980. FIG. 10D shows the
peaks at about 9950, 10250, 11600 and 11800. FIG. 10E shows the
peaks at about 15000, 15200, 15400, 15600 and 15900. FIG. 10F shows
the peaks at about 30000, 31000 and 31800.
[0125] Spectra P1 to P20 (FIGS. 10A-10B) correspond to a batch of
samples from UK, and spectra 1 to 20 (FIGS. 10C-10F) correspond to
a batch of samples from US. The status of the cattle providing the
samples is indicated below in Tables 1 and 2, where negative means
not affected by BSE and positive means BSE-affected cattle.
3 TABLE 1 # Type Status P1 Plasma Negative P2 Plasma Negative P3
Plasma Positive P4 Plasma Negative P5 Plasma Positive P6 Plasma
Positive P7 Plasma Negative P8 Plasma Negative P9 Plasma Positive
P10 Plasma Negative P11 Plasma Positive P12 Plasma Positive P13
Plasma Positive P14 Plasma Positive P15 Plasma Negative P16 Plasma
Negative P17 Plasma Negative P18 Plasma Positive P19 Plasma
Positive P20 Plasma Negative
[0126]
4TABLE 2 # Type Status 1 Plasma Positive 2 Plasma Positive 3 Plasma
Positive 4 Plasma Positive 5 Plasma Positive 6 Plasma Positive 7
Plasma Positive 8 Plasma Positive 9 Plasma Positive 10 Plasma
Positive 11 Plasma Positive 12 Plasma Negative 13 Plasma Negative
14 Plasma Negative 15 Plasma Negative 16 Plasma Negative 17 Plasma
Negative 18 Plasma Negative 19 Plasma Negative 20 Plasma
Negative
[0127] These data demonstrate that the peaks of about 1010, 1100,
1125, 1365, 3645, 4030, 3890, 5820, 7520, 7630, 7980, 9950, 10250,
11600, 11800, 15000, 15200, 15400, 15600, 15900, 30000, 31000 and
31800 Da can be used to diagnose BSE in plasma samples.
EXAMPLE 6
[0128] Identification and Up-Regulation of Cystatin C in CSFs of
CJD-Affected Patients
[0129] CSF samples (100 .mu.l) obtained from the CJD surveillance
unit (sporadic or definite varient of CJD, as well as Not Case)
were investigated using SELDI protein Chip Array technology. WCX2
(a weak cation exchange arrray with carbohydrate functionality),
SAX2 (a strong anion exchange array with quaternary amine
functionality) and IMAC3 (an immobilized metal affinity capture
array with nitrotriacetic acid) surfaces were used in order to
investigate differential specific binding of the proteins in the
samples obtained. Various comparisons were performed between
firstly samples from definite and sporadic cases (CJD samples)
versus corresponding controls (Not Case) in order to discriminate
between samples from patients with CJD symptoms and samples from
patients with similar symptoms which were not CJD (Not
Case=Control). The whole groups of samples from CJD-diagnosed
patients compared with controls from the institute and the
inventors' 14.3.3 samples were analyzed without any distinction in
the diagnosed sub-population. Comparison of these samples did not
allow sporadic and/or variant CJD samples to be distinguished from
their corresponding controls (Not Case).
[0130] The inventors therefore confirmed the presence of a dementia
marker of molecular weight about 13365-13370 (.+-.0.5%), which in
addition to metal affinity also demonstrates cationic
properties.
[0131] The 13365-13370 marker was purified by fractionating the Not
Case CSF samples using anionic exchange chromatography. Spin Sax
columns designed for such fractionation separate proteins according
to their net charge and were used to elute proteins stepwise with
decreasing pI using buffers with increasing salt concentration and
decreasing p1. The protein profiles obtained using both IMAC3 and
SAX chips were similar. Each fraction was loaded on a SDS PAGE for
further identification of the 13350 mw peak. A preparative
colloidal blue-stained Tris-Tricine 1-DE gel was run and stained
with silver nitrate to permit band excision and digestion followed
by mass spectrometry identification. Identification of the squared
bands excised from the gel followed the MALDI-TOF, MALDI-TOF-TOF
(Applied Biosystems: provides partial sequence determination using
collision-induced dissociation fragment analysis) or nanoLC Q-tof
approaches. The 13350 peak was identified as cystatin C.
[0132] Matrix-assisted laser desorption/ionization-time of flight
mass spectrometry (MALDI-TOF MS) is a relatively novel technique in
which a co-precipitate of an UV-light absorbing matrix and a
biomolecule is irradiated by a nanosecond laser pulse. Most of the
laser energy is absorbed by the matrix, which prevents unwanted
fragmentation of the biomolecule. The ionized biomolecules are
accelerated in an electric field and enter the flight tube. During
the flight in this tube, different molecules are separated
according to their mass to charge ratio and reach the detector at
different times. In this way each molecule yields a distinct
signal. The method is used for detection and characterization of
biomolecules, such as proteins, peptides, oligosaccharides and
oligonucleotides, with molecular masses between 400 and 350,000
Da.
[0133] In order to validate the identification and the
up-regulation of cystatin C in CSFs of CJD-affected patients, the
inventors performed Western blot experiments using an antibody
specific for human cystatin C on 8 demented CSF samples versus 8
CSF of CJD-affected patients (3 variant and 5 sporadic CJD).
[0134] FIG. 11 shows the specific increased signal that the
inventors obtained in the 8 CJD-affected patients tested in
comparison to controls, showing that Cystatin provides a
cerebrospinal fluid marker of CJD.
EXAMPLE 7
[0135] Plasma of BSE Affected Cattle: SELDI Analysis.
[0136] Previous comparative studies using SELDI analysis of BSE+
and BSE-plasma samples allowed the inventors to highlight several
protein clusters as being differentially expressed. One such
cluster with a mass centered around 15000 Da was selected for
further analysis, being differentially over-expressed in samples
from BSE-affected cattle. Plasma of BSE-affected cattle was
subjected to one-DE electrophoresis and the band migrating with a
mass of 15000 Da as determined using standard mass marker proteins
was excised, digested with trypsin and subjected to mass
spectrometry by MAL:DI-TOF. By this method the 15000 Da protein
species in the SELDI analysis were putatively identified as
isoforms of bovine hemoglobin.
[0137] In order to investigate and validate the hemoglobin content
of these samples, the inventors looked for antibodies that could
cross react with bovine Hb. A goat polyclonal antibody anti-human
Hb that reacts weakly with equine and bovine hemoglobin (J16,
Biomeda), as well as a sheep polyclonal antibody raised against
native Hb from erythrocytes expected to exhibit cross-reactivity
with Hb from other species (4870-3980, Biotrend-Anawa) were tested.
Experiments were carried out using as positive controls, native
purified human and bovine Hb (4870-4056 and 4870-2002,
Biotrend-Anawa).
[0138] FIG. 12 highlights the Western blot experiments performed
with the goat polyclonal antibody from Biomeda. Besides the strong
signal obtained with human and bovine hemoglobin, an increased
level of a protein at the expected size in the 3 BSE+tested plasma
samples may indeed be observed. The Western blot experiments
performed with the second antibody did not show any signal (data
not shown). Silver stained analytical 2-DE gel (FIG. 13) and an
immunodetection experiment on 2-DE PVDF membranes of BSE-plasma
sample were performed, in order to see if several spots could be
thus detected. The enlarged portion of FIG. 13 shows 4 spots in the
expected area. Two spots seem to correspond to .alpha. chains
(15053 Da, pI 8.19) and 2 others spots seem to correspond to .beta.
chains (15954 Da, pI 7.02). Knowing that the .alpha. chain has 4
putative modification sites consisting of N-glycosylation, Protein
Kinase C Phosphorylation, Casein Kinase 2-Phosphorylation and
N-Myristoylation, as well as .beta. chains having similar ones with
an Amidation site instead of N-glycosylation one (Scan Prosite),
these explain variations in their main molecular weight, as well as
the numerous shoulders highlighted in SELDI spectra.
[0139] To further confirm the identity of the 15000 Da cluster as
isoforms of bovine hemoglobin, bovine and human purified Hb were
analyzed on Normal phase with SELDI. FIG. 14 shows the whole
spectra obtained for both species, illustrating their similarity.
FIGS. 15A and 15B point out within 4 representative spectra, how
much the Hb profile looks like those of BSE+plasma samples on I
MAC, whilst FIG. 15C highlights their difference under 7 kDa. These
spectra led the inventors to conclude that 5 out of the 13 clusters
highlighted in the earlier SELDI study of bovine plasma correspond
to hemoglobin.
[0140] Each of the above cited publications is herein incorporated
by reference to the extent to which it is relied on herein.
Sequence CWU 1
1
2 1 146 PRT Homo sapiens 1 Met Ala Gly Pro Leu Arg Ala Pro Leu Leu
Leu Leu Ala Ile Leu Ala 1 5 10 15 Val Ala Leu Ala Val Ser Pro Ala
Ala Gly Ser Ser Pro Gly Lys Pro 20 25 30 Pro Arg Leu Val Gly Gly
Pro Met Asp Ala Ser Val Glu Glu Glu Gly 35 40 45 Val Arg Arg Ala
Leu Asp Phe Ala Val Gly Glu Tyr Asn Lys Ala Ser 50 55 60 Asn Asp
Met Tyr His Ser Arg Ala Leu Gln Val Val Arg Ala Arg Lys 65 70 75 80
Gln Ile Val Ala Gly Val Asn Tyr Phe Leu Asp Val Glu Leu Gly Arg 85
90 95 Thr Thr Cys Thr Lys Thr Gln Pro Asn Leu Asp Asn Cys Pro Phe
His 100 105 110 Asp Gln Pro His Leu Lys Arg Lys Ala Phe Cys Ser Phe
Gln Ile Tyr 115 120 125 Ala Val Pro Trp Gln Gly Thr Met Thr Leu Ser
Lys Ser Thr Cys Gln 130 135 140 Asp Ala 145 2 120 PRT Homo sapiens
2 Ser Ser Pro Gly Lys Pro Pro Arg Leu Val Gly Gly Pro Met Asp Ala 1
5 10 15 Ser Val Glu Glu Glu Gly Val Arg Arg Ala Leu Asp Phe Ala Val
Gly 20 25 30 Glu Tyr Asn Lys Ala Ser Asn Asp Met Tyr His Ser Arg
Ala Leu Gln 35 40 45 Val Val Arg Ala Arg Lys Gln Ile Val Ala Gly
Val Asn Tyr Phe Leu 50 55 60 Asp Val Glu Leu Gly Arg Thr Thr Cys
Thr Lys Thr Gln Pro Asn Leu 65 70 75 80 Asp Asn Cys Pro Phe His Asp
Gln Pro His Leu Lys Arg Lys Ala Phe 85 90 95 Cys Ser Phe Gln Ile
Tyr Ala Val Pro Trp Gln Gly Thr Met Thr Leu 100 105 110 Ser Lys Ser
Thr Cys Gln Asp Ala 115 120
* * * * *